#!/bin/bash

fsl_deface S15_MPRAGE_UP_0p75_e1.nii.gz defaced_S15_MPRAGE_UP_0p75_e1.nii.gz
fsl_deface S12_MPRAGE_CP_0p8_e1.nii.gz defaced_S12_MPRAGE_CP_0p8_e1.nii.gz
fsl_deface S9_MPRAGE_UP_0p8_e1.nii.gz defaced_S9_MPRAGE_UP_0p8_e1.nii.gz
fsl_deface S4_t1_mp2rage_sag_p3_0.75mm_INV2_e1.nii.gz defaced_S4_t1_mp2rage_sag_p3_0.75mm_INV2_e1.nii.gz -d mask_MP2RAGE.nii

3dcalc -a mask_MP2RAGE.nii -b S3_t1_mp2rage_sag_p3_0.75mm_INV1_e1.nii.gz -prefix defaced_S3_t1_mp2rage_sag_p3_0.75mm_INV1_e1.nii -expr 'a*b'
3dcalc -a mask_MP2RAGE.nii -b S5_t1_mp2rage_sag_p3_0.75mm_T1_Images_e1.nii.gz -prefix defaced_S5_t1_mp2rage_sag_p3_0.75mm_T1_Images_e1.nii -expr 'a*b'
3dcalc -a mask_MP2RAGE.nii -b S6_t1_mp2rage_sag_p3_0.75mm_UNI_Images_e1.nii.gz -prefix defaced_S6_t1_mp2rage_sag_p3_0.75mm_UNI_Images_e1.nii -expr 'a*b'

